post-processing analysis of climate simulation data using python and mpi

Post-processing analysis of climate simulation

data using Python and MPI

John Dennis (dennis@ucar.edu)Dave Brown (dbrown@ucar.edu)

Kevin Paul (kpaul@ucar.edu)Sheri Mickelson (mickelso@ucar.edu)

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Motivation Post-processing consumes a surprisingly large

fraction of simulation time for high-resolution runs

Post-processing analysis is not typically parallelized

Can we parallelize post-processing using existing software?◦ Python ◦ MPI ◦ pyNGL: python interface to NCL graphics◦ pyNIO: python interface to NCL I/O library

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Consider a “piece” of CESM post-processing workflow Conversion of time-slice to time-series Time-slice

◦ Generated by the CESM component model◦ All variables for a particular time-slice in one file

Time-series◦ Form used for some post-processing and CMIP◦ Single variables over a range of model time

Single most expensive post-processing step for CMIP5 submission

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The experiment: Convert 10-years of monthly time-slice files

into time-series files Different methods:

◦ Netcdf Operators (NCO)◦ NCAR Command Language (NCL)◦ Python using pyNIO (NCL I/O library)◦ Climate Data Operators (CDO)◦ ncReshaper-prototype (Fortran + PIO)

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Dataset characteristics:10-years of monthly outputdataset # of 2D vars # of 3D vars Input total size

(Gbytes)CAMFV-1.0 40 82 28.4CAMSE-1.0 43 89 30.8CICE-1.0 117 8.4CAMSE-0.25 101 97 1077.1CLM-1.0 297 9.0CLM-0.25 150 84.0CICE-0.1 114 569.6POP-0.1 23 11 3183.8POP-1.0 78 36 194.4

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Duration: Serial NCO

14 hours!

5 hours

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Throughput: Serial methods

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Approaches to Parallelism Data-parallelism:

◦ Divide single variable across multiple ranks◦ Parallelism used by large simulation codes: CESM,

WRF, etc◦ Approach used by ncReshaper-prototype code

Task-parallelism:◦ Divide independent tasks across multiple ranks◦ Climate models output large number of different

variables T, U, V, W, PS, etc..

◦ Approach used by python + MPI code

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Single source Python approach Create dictionary which describes which

tasks need to be performed Partition dictionary across MPI ranks Utility module ‘parUtils.py’ only difference

between parallel and serial execution

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Example python code import parUtils as par…rank = par.GetRank()# construct global dictionary ‘varsTimeseries’ for all

variablesvarsTimeseries = ConstructDict()…# Partition dictionary into local piecelvars = par.Partition(varsTimeseries)# Iterate over all variables assigned to MPI rankfor k,v in lvars.iteritems():

….

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Throughput: Parallel methods(4 nodes, 16 cores)

task-parallelism data-parallelism

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Throughput:pyNIO + MPI w/compression

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Duration: NCO versus pyNIO + MPI w/compression

7.9x (3 nodes)

35x speedup (13 nodes)

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Conclusions Large amounts of “easy-parallelism”

present in post-processing operations Single source python scripts can be written

to achieve task-parallel execution Factors of 8 – 35x speedup is possible Need ability to exploit both task and data

parallelism Exploring broader use within CESM workflow

Expose entire NCL capability to python?